5DC4

CRYSTAL STRUCTURE OF MONOBODY AS25/ABL1 SH2 DOMAIN COMPLEX, CRYSTAL A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface.

Wojcik, J.Lamontanara, A.J.Grabe, G.Koide, A.Akin, L.Gerig, B.Hantschel, O.Koide, S.

(2016) J Biol Chem 291: 8836-8847

  • DOI: 10.1074/jbc.M115.707901
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bcr-Abl is a constitutively active kinase that causes chronic myelogenous leukemia. We have shown that a tandem fusion of two designed binding proteins, termed monobodies, directed to the interaction interface between the Src homology 2 (SH2) and kin ...

    Bcr-Abl is a constitutively active kinase that causes chronic myelogenous leukemia. We have shown that a tandem fusion of two designed binding proteins, termed monobodies, directed to the interaction interface between the Src homology 2 (SH2) and kinase domains and to the phosphotyrosine-binding site of the SH2 domain, respectively, inhibits the Bcr-Abl kinase activity. Because the latter monobody inhibits processive phosphorylation by Bcr-Abl and the SH2-kinase interface is occluded in the active kinase, it remained undetermined whether targeting the SH2-kinase interface alone was sufficient for Bcr-Abl inhibition. To address this question, we generated new, higher affinity monobodies with single nanomolar KD values targeting the kinase-binding surface of SH2. Structural and mutagenesis studies revealed the molecular underpinnings of the monobody-SH2 interactions. Importantly, the new monobodies inhibited Bcr-Abl kinase activity in vitro and in cells, and they potently induced cell death in chronic myelogenous leukemia cell lines. This work provides strong evidence for the SH2-kinase interface as a pharmacologically tractable site for allosteric inhibition of Bcr-Abl.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, Shohei.Koide@nyumc.org.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ABL1
A
123Homo sapiensMutation(s): 0 
Gene Names: ABL1ABLJTK7
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Go to UniProtKB:  P00519
NIH Common Fund Data Resources
PHAROS  P00519

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AS25 monobody
B
95Homo sapiensMutation(s): 0 
Gene Names: FN1FN
Find proteins for P02751 (Homo sapiens)
Go to UniProtKB:  P02751
NIH Common Fund Data Resources
PHAROS  P02751
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.281α = 90
b = 74.928β = 90
c = 39.229γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM090324
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM07281
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA014599

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Data collection
  • Version 1.2: 2016-05-11
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence